RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.LMCLfC/RM_2390963.WedApr160454202025 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1744804457 Database = /data/tmp/rModeler.LMCLfC/GCA_965140275.1_rCarCar1.hap2 - Sequences = 33 - Bases = 2206382585 Storage Throughput = excellent ( 1236.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022688 bp ( 40022688 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:03:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:30 (hh:mm:ss) Elapsed Time Round Time: 00:30:35 (hh:mm:ss) Elapsed Time : 487 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13095 repeats masked totaling 3103337 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021180 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10021180 bp After Masking: 6853920 bp Masked: 31.61 % -- Input Database Coverage: 10021180 bp out of 2206382585 bp ( 0.45 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:12 (hh:mm:ss) Elapsed Time, 16742 HSPs Collected Number of families returned by RECON: 1740 Round Time: 00:17:11 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42094 repeats masked totaling 9584847 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001428 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30001428 bp After Masking: 20217644 bp Masked: 32.61 % -- Input Database Coverage: 40022608 bp out of 2206382585 bp ( 1.81 % ) Sampling Time: 00:04:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:24:42 (hh:mm:ss) Elapsed Time, 118860 HSPs Collected Number of families returned by RECON: 5201 Round Time: 00:41:52 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 147449 repeats masked totaling 32669228 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003956 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90003242 bp After Masking: 56653845 bp Masked: 37.05 % -- Input Database Coverage: 130026564 bp out of 2206382585 bp ( 5.89 % ) Sampling Time: 00:12:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:21:56 (hh:mm:ss) Elapsed Time, 775451 HSPs Collected Number of families returned by RECON: 14447 Round Time: 03:15:45 (hh:mm:ss) Elapsed Time : 431 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 513326 repeats masked totaling 113869947 bp(s). - TE Masking time 00:08:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270084038 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 270027856 bp After Masking: 154162832 bp Masked: 42.91 % -- Input Database Coverage: 400110602 bp out of 2206382585 bp ( 18.13 % ) Sampling Time: 00:42:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 16:05:48 (hh:mm:ss) Elapsed Time, 1590211 HSPs Collected Number of families returned by RECON: 43621 Round Time: 19:18:25 (hh:mm:ss) Elapsed Time : 1018 families discovered. RepeatScout/RECON discovery complete: 2115 families found Classification Time: 01:19:15 (hh:mm:ss) Elapsed Time Program Time: 25:23:03 (hh:mm:ss) Elapsed Time